diff --git a/.nf-core.yml b/.nf-core.yml index bcfe64b6..d54c5434 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -24,4 +24,4 @@ template: - fastqc - multiqc - igenomes - version: 4.1.2 + version: 5.0.0 diff --git a/CHANGELOG.md b/CHANGELOG.md index b1bbe481..7f452c0f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,41 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## [[5.0.0](https://github.com/nf-core/pixelator/releases/tag/5.0.0)] - 2026-07-13 + +### Changed + +- **(breaking change)** Rename `pna_sample_calling_confidence_threshold` to `pna_sample_calling_enrichment_threshold` to match pixelator 0.29.0. By @elhb [#227](https://github.com/nf-core/pixelator/pull/227) +- Change default layout algorithm from `wpmds_3d` to `coarsened_pmds_3d`. By @elhb [#227](https://github.com/nf-core/pixelator/pull/227) +- Change `pna_graph_refinement_stage_leiden_resolution` and `pna_graph_refinement_stage_max_edges_to_remove` default values + to 0.5, and 20 respectively based on latest evaluations. By @ptajvar [#226](https://github.com/nf-core/pixelator/pull/226) +- Expose `pna_graph_component_size_max_threshold`. By @Aratz [#233](https://github.com/nf-core/pixelator/pull/233) + +### Enhancements & fixes + +- Update pixelator container to 0.29.0. By @elhb [#227](https://github.com/nf-core/pixelator/pull/227) +- Update pixelatorES to 0.11.2. By @elhb [#227](https://github.com/nf-core/pixelator/pull/227) +- Condense ES script. By @Aratz [#232](https://github.com/nf-core/pixelator/pull/232) + +### Software dependencies + +| Dependency | Old version | New version | +| ------------- | ----------- | ----------- | +| `pixelator` | 0.28.0 | 0.29.0 | +| `pixelatorES` | 0.10.4 | 0.11.2 | + +### Parameters + +| Old parameter | New parameter | +| ----------------------------------------- | ----------------------------------------- | +| `pna_sample_calling_confidence_threshold` | `pna_sample_calling_enrichment_threshold` | +| | `pna_graph_component_size_max_threshold` | + +> [!NOTE] +> Parameter has been **updated** if both old and new parameter information is present. +> Parameter has been **added** if just the new parameter information is present. +> Parameter has been **removed** if new parameter information isn't present. + ## [[4.1.2](https://github.com/nf-core/pixelator/releases/tag/4.1.2)] - 2026-06-04 ### Enhancements & fixes diff --git a/conf/modules.pna.config b/conf/modules.pna.config index 6eed0daf..9947bfef 100644 --- a/conf/modules.pna.config +++ b/conf/modules.pna.config @@ -132,6 +132,7 @@ process { params.pna_graph_initial_stage_max_edges_to_remove_relative ? "--initial-stage-max-edges-to-remove-relative ${params.pna_graph_initial_stage_max_edges_to_remove_relative}" : '', params.pna_graph_refinement_stage_max_edges_to_remove_relative ? "--refinement-stage-max-edges-to-remove-relative ${params.pna_graph_refinement_stage_max_edges_to_remove_relative}" : '', params.pna_graph_component_size_min_threshold ? "--component-size-min-threshold ${params.pna_graph_component_size_min_threshold}" : '', + params.pna_graph_component_size_max_threshold ? "--component-size-max-threshold ${params.pna_graph_component_size_max_threshold}" : '', ].join(' ').trim() } publishDir = [ @@ -160,7 +161,7 @@ process { [ params.pna_sample_calling_remove_incompatible ? "--remove-incompatible" : '', params.pna_sample_calling_save_undetermined ? "--save-undetermined" : '', - params.pna_sample_calling_confidence_threshold != null ? "--confidence-threshold ${params.pna_sample_calling_confidence_threshold}" : '', + params.pna_sample_calling_enrichment_threshold != null ? "--enrichment-threshold ${params.pna_sample_calling_enrichment_threshold}" : '', ].join(' ').trim() } publishDir = [ diff --git a/conf/test_proxiome_v1.config b/conf/test_proxiome_v1.config index afe193a4..ef029529 100644 --- a/conf/test_proxiome_v1.config +++ b/conf/test_proxiome_v1.config @@ -17,9 +17,15 @@ params { // Input data input = params.pipelines_testdata_base_path + '/samplesheet/pna/samplesheet_proxiome_v1.csv' - input_basedir = params.pipelines_testdata_base_path + '/testdata/pna' + input_basedir = params.pipelines_testdata_base_path + '/new-test-data/pna' - pna_graph_component_size_min_threshold = 100 + // Synthetic data was generated to pass with the test with lower than default resolution + pna_graph_refinement_stage_leiden_resolution = 0.01 + pna_graph_component_size_min_threshold = 100 + + // Synthetic nf-core test datasets include components too small for + // coarsened_pmds_3d. Keep wpmds_3d in test profiles. + pna_layout_layout_algorithm = "wpmds_3d" skip_layout = false technology = "proxiome-v1" diff --git a/conf/test_proxiome_v2.config b/conf/test_proxiome_v2.config index 7273a4df..406de6a7 100644 --- a/conf/test_proxiome_v2.config +++ b/conf/test_proxiome_v2.config @@ -16,10 +16,16 @@ params { config_profile_description = 'Minimal test dataset to check pipeline function' // Input data - input = params.pipelines_testdata_base_path + '/samplesheet/pna/samplesheet_proxiome_v2.csv' - input_basedir = params.pipelines_testdata_base_path + '/testdata/pna' + input = params.pipelines_testdata_base_path + '/new-test-data/samplesheet/pna/samplesheet_proxiome_v2.csv' + input_basedir = params.pipelines_testdata_base_path + '/new-test-data/pna' - pna_graph_component_size_min_threshold = 100 + // Synthetic data was generated to pass with the test with lower than default resolution + pna_graph_refinement_stage_leiden_resolution = 0.01 + pna_graph_component_size_min_threshold = 100 + + // Synthetic nf-core test datasets include components too small for + // coarsened_pmds_3d. Keep wpmds_3d in test profiles. + pna_layout_layout_algorithm = "wpmds_3d" skip_layout = false technology = "proxiome-v2" diff --git a/docs/images/nf-core-pixelator-metromap.svg b/docs/images/nf-core-pixelator-metromap.svg index 1d1c8a2e..870f814d 100644 --- a/docs/images/nf-core-pixelator-metromap.svg +++ b/docs/images/nf-core-pixelator-metromap.svg @@ -1,14 +1,14 @@ - + - + - + @@ -18,15 +18,15 @@ - + - - - - + + + + - + @@ -34,18 +34,18 @@ - + - + - + - + @@ -79,10 +79,10 @@ - - + + - + @@ -94,7 +94,7 @@ - + @@ -112,19 +112,19 @@ - - - - - - - - - - - - - + + + + + + + + + + + + + @@ -141,119 +141,119 @@ - + - + - + - + - - + + - + - + - + - + - - + + - + - + - + - + - - + + - + - + - + - + - - + + - + - + - + - + - - + + - + - + - + - + - + - + - + diff --git a/docs/output.md b/docs/output.md index d4af8cc6..17d13fee 100644 --- a/docs/output.md +++ b/docs/output.md @@ -151,9 +151,10 @@ This step uses the `pixelator single-cell-pna sample-calling` command. It takes the graph PXL file and the sample sheet as input and assigns each component to the most likely sample in pooled experiments. -Components with assignment confidence below the selected threshold are marked -as undetermined and can be saved to a separate output file. The resulting -per-sample dehashed PXL files are then used as input for the analysis step. +Components with sample enrichment below `pna_sample_calling_enrichment_threshold` +(default 10.0) are marked as undetermined and can be saved to a separate output +file. The resulting per-sample dehashed PXL files are then used as input for +the analysis step.
Output files diff --git a/modules/local/experiment_summary/main.nf b/modules/local/experiment_summary/main.nf index 6cc5053e..2bc2d3e4 100644 --- a/modules/local/experiment_summary/main.nf +++ b/modules/local/experiment_summary/main.nf @@ -4,8 +4,8 @@ process EXPERIMENT_SUMMARY { label "error_retry" container "${params.experiment_summary_container?: workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'quay.io/pixelgen-technologies/pixelatores:0.10.4' - : 'quay.io/pixelgen-technologies/pixelatores:0.10.4'}" + ? 'quay.io/pixelgen-technologies/pixelatores:0.11.2' + : 'quay.io/pixelgen-technologies/pixelatores:0.11.2'}" input: path samplesheet_path @@ -22,17 +22,24 @@ process EXPERIMENT_SUMMARY { assert results_data instanceof List : "Expected results_data to be a List, got ${results_data?.getClass()?.simpleName ?: 'null'}" assert results_data.size() == result_stages.size(): "Mismatch between result files (${results_data.size()}) and stage labels (${result_stages.size()})" - def stageCopies = [result_stages, results_data].transpose().collect { stage, file -> - """ - mkdir -p "results/${stage}" - ln -s "../../${file}" "results/${stage}/" - """ - }.join('\n') + def stageArray = result_stages.collect { "\"${it}\"" }.join(' ') """ # Copy the full quarto dir from the read-only image into the workdir cp -r /workspace/inst/quarto/ ./quarto/ mkdir -p results - ${stageCopies} + + # Stage each result file into results//. Files are staged into + # results_raw/1, results_raw/2, ... in the same order as the stage names. + stages=(${stageArray}) + for i in "\${!stages[@]}"; do + idx=\$((i + 1)) + dest="results/\${stages[\$i]}" + mkdir -p "\$dest" + for f in "results_raw/\${idx}"/*; do + ln -s "../../\$f" "\$dest/" + done + done + quarto render ./quarto/pixelatorES.qmd \\ -P sample_sheet="\$PWD/${samplesheet_path}" \\ -P data_folder="\$PWD/results/" \\ diff --git a/modules/local/experiment_summary/tests/main.nf.test b/modules/local/experiment_summary/tests/main.nf.test index 20b6e58e..8f40c532 100644 --- a/modules/local/experiment_summary/tests/main.nf.test +++ b/modules/local/experiment_summary/tests/main.nf.test @@ -17,15 +17,15 @@ nextflow_process { when { process { """ - input[0] = [ file(params.pipelines_testdata_base_path + 'samplesheet/pna/samplesheet_proxiome_v2.csv', checkIfExists: true) ] + input[0] = [ file(params.pipelines_testdata_base_path + 'new-test-data/samplesheet/pna/samplesheet_proxiome_v2.csv', checkIfExists: true) ] input[1] = [ - [id:'all', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v2.0', technology:'proxiome-v2' ], + [id:'all', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-prerelease', technology:'proxiome-v2' ], [ 'amplicon', 'amplicon', ], [ - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/pool1.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/pool1.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/amplicon/pool1.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/amplicon/pool1.report.json', checkIfExists: true), ] ] """ @@ -53,84 +53,80 @@ nextflow_process { } process { """ - input[0] = [ file(params.pipelines_testdata_base_path + 'samplesheet/pna/samplesheet_proxiome_v2.csv', checkIfExists: true) ] + input[0] = [ file(params.pipelines_testdata_base_path + 'new-test-data/samplesheet/pna/samplesheet_proxiome_v2.csv', checkIfExists: true) ] input[1] = [ - [id:'all', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v2.0', technology:'proxiome-v2' ], + [id:'all', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-prerelease', technology:'proxiome-v2' ], [ 'amplicon', 'amplicon', 'amplicon', 'amplicon', 'demux', 'demux', 'demux', 'demux', 'collapse', 'collapse', 'collapse', 'collapse', 'graph', 'graph', 'graph', 'graph', 'graph', 'graph', - 'denoise', 'denoise', 'denoise', 'denoise', 'denoise', 'denoise', 'denoise', 'denoise', + 'denoise', 'denoise', 'denoise', 'denoise', 'analysis', 'analysis', 'analysis', 'analysis', 'analysis', 'analysis', 'analysis', 'analysis', 'layout', 'layout', 'layout', 'layout', 'layout', 'layout', 'layout', 'layout', 'layout', 'layout', 'layout', 'layout', 'sample_calling', 'sample_calling', 'sample_calling', 'sample_calling', 'sample_calling', 'sample_calling', 'sample_calling', 'sample_calling', 'sample_calling', 'sample_calling', 'sample_calling', 'sample_calling', 'sample_calling', 'sample_calling', 'sample_calling', 'sample_calling', 'sample_calling', 'sample_calling', ], [ - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/pool1.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/pool1.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/pool2.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/pool2.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/pool1.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/pool1.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/pool2.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/pool2.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/pool1.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/pool1.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/pool2.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/pool2.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/pool1.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/pool1.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/pool2.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/pool2.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/pool1.graph.pxl', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/pool2.graph.pxl', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/sample1.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/sample1.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/sample2.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/sample2.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/sample3.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/sample3.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/sample4.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/sample4.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/sample1.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/sample1.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/sample2.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/sample2.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/sample3.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/sample3.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/sample4.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/sample4.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/sample1.layout.pxl', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/sample1.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/sample1.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/sample2.layout.pxl', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/sample2.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/sample2.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/sample3.layout.pxl', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/sample3.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/sample3.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/sample4.layout.pxl', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/sample4.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/sample4.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/pool1.sample_calling.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/pool1_undetermined.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/pool1_undetermined.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/pool2.sample_calling.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/pool2_undetermined.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/pool2_undetermined.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/sample1.dehashed.pxl', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/sample1.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/sample1.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/sample2.dehashed.pxl', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/sample2.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/sample2.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/sample3.dehashed.pxl', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/sample3.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/sample3.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/sample4.dehashed.pxl', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/sample4.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/sample4.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/amplicon/pool1.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/amplicon/pool1.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/amplicon/pool2.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/amplicon/pool2.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/demux/pool1.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/demux/pool1.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/demux/pool2.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/demux/pool2.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/collapse/pool1.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/collapse/pool1.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/collapse/pool2.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/collapse/pool2.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/graph/pool1.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/graph/pool1.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/graph/pool2.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/graph/pool2.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/graph/pool1.graph.pxl', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/graph/pool2.graph.pxl', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/denoise/pool1.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/denoise/pool1.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/denoise/pool2.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/denoise/pool2.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/analysis/sample1.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/analysis/sample1.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/analysis/sample2.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/analysis/sample2.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/analysis/sample3.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/analysis/sample3.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/analysis/sample4.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/analysis/sample4.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/layout/sample1.layout.pxl', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/layout/sample1.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/layout/sample1.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/layout/sample2.layout.pxl', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/layout/sample2.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/layout/sample2.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/layout/sample3.layout.pxl', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/layout/sample3.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/layout/sample3.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/layout/sample4.layout.pxl', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/layout/sample4.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/layout/sample4.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/sample_calling/pool1.sample_calling.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/sample_calling/pool1_undetermined.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/sample_calling/pool1_undetermined.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/sample_calling/pool2.sample_calling.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/sample_calling/pool2_undetermined.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/sample_calling/pool2_undetermined.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/sample_calling/sample1.dehashed.pxl', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/sample_calling/sample1.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/sample_calling/sample1.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/sample_calling/sample2.dehashed.pxl', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/sample_calling/sample2.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/sample_calling/sample2.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/sample_calling/sample3.dehashed.pxl', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/sample_calling/sample3.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/sample_calling/sample3.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/sample_calling/sample4.dehashed.pxl', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/sample_calling/sample4.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/sample_calling/sample4.report.json', checkIfExists: true), ] ] """ diff --git a/modules/local/experiment_summary/tests/main.nf.test.snap b/modules/local/experiment_summary/tests/main.nf.test.snap index 41f08551..5c1ed3e8 100644 --- a/modules/local/experiment_summary/tests/main.nf.test.snap +++ b/modules/local/experiment_summary/tests/main.nf.test.snap @@ -11,11 +11,11 @@ [ "EXPERIMENT_SUMMARY", "experiment-summary", - "0.10.4 " + "0.11.2 " ] ] ], - "timestamp": "2026-05-27T13:29:18.163301309", + "timestamp": "2026-06-17T08:45:43.718413469", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.5" @@ -27,14 +27,14 @@ [ "EXPERIMENT_SUMMARY", "experiment-summary", - "0.10.4 " + "0.11.2 " ] ] ], - "timestamp": "2026-05-27T13:28:01.67719335", + "timestamp": "2026-06-17T08:44:46.211800729", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.5" } } -} \ No newline at end of file +} diff --git a/modules/local/pixelator/amplicon/main.nf b/modules/local/pixelator/amplicon/main.nf index 991851d5..7ecf37d5 100644 --- a/modules/local/pixelator/amplicon/main.nf +++ b/modules/local/pixelator/amplicon/main.nf @@ -5,8 +5,8 @@ process PIXELATOR_AMPLICON { // TODO: Add conda // conda "bioconda::pixelator=0.18.2" container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'quay.io/pixelgen-technologies/pixelator:0.28.0' - : 'quay.io/pixelgen-technologies/pixelator:0.28.0'}" + ? 'quay.io/pixelgen-technologies/pixelator:0.29.0' + : 'quay.io/pixelgen-technologies/pixelator:0.29.0'}" input: tuple val(meta), path(reads, arity: '1..*') diff --git a/modules/local/pixelator/amplicon/tests/main.nf.test b/modules/local/pixelator/amplicon/tests/main.nf.test index 00d6ccf2..6a0b8e6d 100644 --- a/modules/local/pixelator/amplicon/tests/main.nf.test +++ b/modules/local/pixelator/amplicon/tests/main.nf.test @@ -15,10 +15,10 @@ nextflow_process { process { """ input[0] = [ - [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v2.0', technology:'proxiome-v2' ], + [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-prerelease', technology:'proxiome-v2' ], [ - file(params.pipelines_testdata_base_path + 'testdata/pna/fastq/pool1_R1.fastq.gz', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/fastq/pool1_R2.fastq.gz', checkIfExists: true) + file(params.pipelines_testdata_base_path + 'new-test-data/pna/fastq/pool1_R1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/fastq/pool1_R2.fastq.gz', checkIfExists: true) ] ] """ @@ -41,10 +41,10 @@ nextflow_process { process { """ input[0] = [ - [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v2.0', technology:'proxiome-v2' ], + [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-prerelease', technology:'proxiome-v2' ], [ - file(params.pipelines_testdata_base_path + 'testdata/pna/fastq/pool1_R1.fastq.gz', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/fastq/pool1_R2.fastq.gz', checkIfExists: true) + file(params.pipelines_testdata_base_path + 'new-test-data/pna/fastq/pool1_R1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/fastq/pool1_R2.fastq.gz', checkIfExists: true) ] ] """ diff --git a/modules/local/pixelator/amplicon/tests/main.nf.test.snap b/modules/local/pixelator/amplicon/tests/main.nf.test.snap index fc57d4bb..722e9aa6 100644 --- a/modules/local/pixelator/amplicon/tests/main.nf.test.snap +++ b/modules/local/pixelator/amplicon/tests/main.nf.test.snap @@ -7,7 +7,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.amplicon.fq.zst:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -18,7 +18,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -29,7 +29,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -40,7 +40,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.pixelator-amplicon.log:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -60,7 +60,7 @@ [ "PIXELATOR_AMPLICON", "pixelator", - "0.28.0" + "0.29.0" ] ], "amplicon": [ @@ -68,7 +68,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.amplicon.fq.zst:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -79,7 +79,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.pixelator-amplicon.log:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -90,7 +90,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -101,7 +101,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -111,15 +111,15 @@ [ "PIXELATOR_AMPLICON", "pixelator", - "0.28.0" + "0.29.0" ] ] } ], - "timestamp": "2026-05-29T14:05:38.535137938", + "timestamp": "2026-06-17T09:02:16.432856152", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.2" + "nextflow": "25.10.5" } }, "PNA amplicon - small test": { @@ -140,11 +140,11 @@ [ "PIXELATOR_AMPLICON", "pixelator", - "0.28.0" + "0.29.0" ] ] ], - "timestamp": "2026-05-27T13:29:36.579458417", + "timestamp": "2026-06-17T09:02:44.504317584", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.5" diff --git a/modules/local/pixelator/analysis/main.nf b/modules/local/pixelator/analysis/main.nf index 96c727ef..060bd1fd 100644 --- a/modules/local/pixelator/analysis/main.nf +++ b/modules/local/pixelator/analysis/main.nf @@ -6,8 +6,8 @@ process PIXELATOR_ANALYSIS { // conda "bioconda::pixelator=0.18.2" container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'quay.io/pixelgen-technologies/pixelator:0.28.0' - : 'quay.io/pixelgen-technologies/pixelator:0.28.0'}" + ? 'quay.io/pixelgen-technologies/pixelator:0.29.0' + : 'quay.io/pixelgen-technologies/pixelator:0.29.0'}" input: tuple val(meta), path(data) diff --git a/modules/local/pixelator/analysis/tests/main.nf.test b/modules/local/pixelator/analysis/tests/main.nf.test index 8dc9d5e3..6973c936 100644 --- a/modules/local/pixelator/analysis/tests/main.nf.test +++ b/modules/local/pixelator/analysis/tests/main.nf.test @@ -15,8 +15,8 @@ nextflow_process { process { """ input[0] = [ - [ id:'sample1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v2.0', technology:'proxiome-v2' ], - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/sample1.dehashed.pxl', checkIfExists: true), + [ id:'sample1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-prerelease', technology:'proxiome-v2' ], + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/sample_calling/sample1.dehashed.pxl', checkIfExists: true), ] """ } @@ -38,8 +38,8 @@ nextflow_process { process { """ input[0] = [ - [ id:'sample1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v2.0', technology:'proxiome-v2' ], - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/sample1.dehashed.pxl', checkIfExists: true), + [ id:'sample1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-prerelease', technology:'proxiome-v2' ], + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/sample_calling/sample1.dehashed.pxl', checkIfExists: true), ] """ } diff --git a/modules/local/pixelator/analysis/tests/main.nf.test.snap b/modules/local/pixelator/analysis/tests/main.nf.test.snap index c0e533d1..b1329ef3 100644 --- a/modules/local/pixelator/analysis/tests/main.nf.test.snap +++ b/modules/local/pixelator/analysis/tests/main.nf.test.snap @@ -17,11 +17,11 @@ [ "PIXELATOR_ANALYSIS", "pixelator", - "0.28.0" + "0.29.0" ] ] ], - "timestamp": "2026-05-27T13:30:22.208787114", + "timestamp": "2026-06-17T09:03:34.334645405", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.5" @@ -35,7 +35,7 @@ { "id": "sample1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "sample1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -46,7 +46,7 @@ { "id": "sample1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "sample1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -57,7 +57,7 @@ { "id": "sample1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "sample1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -68,7 +68,7 @@ { "id": "sample1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, [ @@ -83,7 +83,7 @@ { "id": "sample1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "sample1.pixelator-analysis.log:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -103,7 +103,7 @@ [ "PIXELATOR_ANALYSIS", "pixelator", - "0.28.0" + "0.29.0" ] ], "all_results": [ @@ -111,7 +111,7 @@ { "id": "sample1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, [ @@ -126,7 +126,7 @@ { "id": "sample1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "sample1.pixelator-analysis.log:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -137,7 +137,7 @@ { "id": "sample1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "sample1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -148,7 +148,7 @@ { "id": "sample1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "sample1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -159,7 +159,7 @@ { "id": "sample1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "sample1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -169,15 +169,15 @@ [ "PIXELATOR_ANALYSIS", "pixelator", - "0.28.0" + "0.29.0" ] ] } ], - "timestamp": "2026-05-29T14:06:25.604853005", + "timestamp": "2026-06-17T09:02:53.51770839", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.2" + "nextflow": "25.10.5" } } } \ No newline at end of file diff --git a/modules/local/pixelator/collapse/main.nf b/modules/local/pixelator/collapse/main.nf index f90ca932..087ac781 100644 --- a/modules/local/pixelator/collapse/main.nf +++ b/modules/local/pixelator/collapse/main.nf @@ -7,8 +7,8 @@ process PIXELATOR_COLLAPSE { // TODO: Add conda // conda "bioconda::pixelator=0.18.2" container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'quay.io/pixelgen-technologies/pixelator:0.28.0' - : 'quay.io/pixelgen-technologies/pixelator:0.28.0'}" + ? 'quay.io/pixelgen-technologies/pixelator:0.29.0' + : 'quay.io/pixelgen-technologies/pixelator:0.29.0'}" input: tuple val(meta), path(reads), path(panel_file), val(panel), val(design) diff --git a/modules/local/pixelator/collapse/tests/main.nf.test b/modules/local/pixelator/collapse/tests/main.nf.test index 40a833d1..ca43cf1f 100644 --- a/modules/local/pixelator/collapse/tests/main.nf.test +++ b/modules/local/pixelator/collapse/tests/main.nf.test @@ -15,12 +15,12 @@ nextflow_process { process { """ input[0] = [ - [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v2.0', technology:'proxiome-v2' ], + [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-prerelease', technology:'proxiome-v2' ], [ - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/pool1.demux.m1.part_000.parquet', checkIfExists: true) + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/demux/pool1.demux.m1.part_000.parquet', checkIfExists: true) ], [], // panel_file - 'proxiome-v2-immuno-155-v2.0', // panel + 'proxiome-v2-immuno-155-prerelease', // panel 'proxiome-v2' // design ] """ @@ -43,12 +43,12 @@ nextflow_process { process { """ input[0] = [ - [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v2.0', technology:'proxiome-v2' ], + [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-prerelease', technology:'proxiome-v2' ], [ - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/pool1.demux.m1.part_000.parquet', checkIfExists: true) + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/demux/pool1.demux.m1.part_000.parquet', checkIfExists: true) ], [], // panel_file - 'proxiome-v2-immuno-155-v2.0', // panel + 'proxiome-v2-immuno-155-prerelease', // panel 'proxiome-v2' // design ] """ @@ -78,13 +78,13 @@ nextflow_process { process { """ input[0] = [ - [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v2.0', technology:'proxiome-v2' ], + [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-prerelease', technology:'proxiome-v2' ], [ - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/pool1.demux.m1.part_000.parquet', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/pool1.demux.m2.part_000.parquet', checkIfExists: true) + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/demux/pool1.demux.m1.part_000.parquet', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/demux/pool1.demux.m2.part_000.parquet', checkIfExists: true) ], [], // panel_file - 'proxiome-v2-immuno-155-v2.0', // panel + 'proxiome-v2-immuno-155-prerelease', // panel 'proxiome-v2' // design ] """ diff --git a/modules/local/pixelator/collapse/tests/main.nf.test.snap b/modules/local/pixelator/collapse/tests/main.nf.test.snap index f48263e8..eeb5c971 100644 --- a/modules/local/pixelator/collapse/tests/main.nf.test.snap +++ b/modules/local/pixelator/collapse/tests/main.nf.test.snap @@ -17,11 +17,11 @@ [ "PIXELATOR_COLLAPSE", "pixelator", - "0.28.0" + "0.29.0" ] ] ], - "timestamp": "2026-05-27T13:30:52.660008481", + "timestamp": "2026-06-17T09:04:06.511763997", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.5" @@ -35,7 +35,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, [ @@ -48,7 +48,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, [ @@ -61,7 +61,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.demux.m1.part_000.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -72,7 +72,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.demux.m1.part_000.pixelator-collapse.log:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -92,7 +92,7 @@ [ "PIXELATOR_COLLAPSE", "pixelator", - "0.28.0" + "0.29.0" ] ], "collapsed": [ @@ -100,7 +100,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, [ @@ -113,7 +113,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.demux.m1.part_000.pixelator-collapse.log:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -124,7 +124,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.demux.m1.part_000.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -135,7 +135,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, [ @@ -147,15 +147,15 @@ [ "PIXELATOR_COLLAPSE", "pixelator", - "0.28.0" + "0.29.0" ] ] } ], - "timestamp": "2026-05-29T14:07:42.503855734", + "timestamp": "2026-06-17T09:03:46.654816459", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.2" + "nextflow": "25.10.5" } }, "PNA collapse - small test - multiple files": { diff --git a/modules/local/pixelator/combine_collapse/main.nf b/modules/local/pixelator/combine_collapse/main.nf index c0c0bf63..333614c8 100644 --- a/modules/local/pixelator/combine_collapse/main.nf +++ b/modules/local/pixelator/combine_collapse/main.nf @@ -6,8 +6,8 @@ process PIXELATOR_COMBINE_COLLAPSE { // conda "bioconda::pixelator=0.18.2" container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'quay.io/pixelgen-technologies/pixelator:0.28.0' - : 'quay.io/pixelgen-technologies/pixelator:0.28.0'}" + ? 'quay.io/pixelgen-technologies/pixelator:0.29.0' + : 'quay.io/pixelgen-technologies/pixelator:0.29.0'}" input: tuple val(meta), path(parquet_files, stageAs: "parquet/*"), path(json_report_files, stageAs: "reports/*") diff --git a/modules/local/pixelator/combine_collapse/tests/main.nf.test b/modules/local/pixelator/combine_collapse/tests/main.nf.test index 241fe444..0c159e17 100644 --- a/modules/local/pixelator/combine_collapse/tests/main.nf.test +++ b/modules/local/pixelator/combine_collapse/tests/main.nf.test @@ -17,14 +17,14 @@ nextflow_process { process { """ input[0] = [ - [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v2.0', technology:'proxiome-v2' ], + [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-prerelease', technology:'proxiome-v2' ], [ - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/pool1.collapse.m1.part_000.parquet', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/pool1.collapse.m2.part_000.parquet', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/collapse/pool1.collapse.m1.part_000.parquet', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/collapse/pool1.collapse.m2.part_000.parquet', checkIfExists: true), ], [ - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/pool1.collapse.m1.part_000.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/pool1.collapse.m2.part_000.report.json', checkIfExists: true) + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/collapse/pool1.collapse.m1.part_000.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/collapse/pool1.collapse.m2.part_000.report.json', checkIfExists: true) ] ] """ @@ -48,14 +48,14 @@ nextflow_process { process { """ input[0] = [ - [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v2.0', technology:'proxiome-v2' ], + [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-prerelease', technology:'proxiome-v2' ], [ - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/pool1.collapse.m1.part_000.parquet', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/pool1.collapse.m2.part_000.parquet', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/collapse/pool1.collapse.m1.part_000.parquet', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/collapse/pool1.collapse.m2.part_000.parquet', checkIfExists: true), ], [ - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/pool1.collapse.m1.part_000.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/pool1.collapse.m2.part_000.report.json', checkIfExists: true) + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/collapse/pool1.collapse.m1.part_000.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/collapse/pool1.collapse.m2.part_000.report.json', checkIfExists: true) ] ] """ diff --git a/modules/local/pixelator/combine_collapse/tests/main.nf.test.snap b/modules/local/pixelator/combine_collapse/tests/main.nf.test.snap index 82e2bd96..39415a2a 100644 --- a/modules/local/pixelator/combine_collapse/tests/main.nf.test.snap +++ b/modules/local/pixelator/combine_collapse/tests/main.nf.test.snap @@ -16,11 +16,11 @@ [ "PIXELATOR_COMBINE_COLLAPSE", "pixelator", - "0.28.0" + "0.29.0" ] ] ], - "timestamp": "2026-05-27T13:31:49.320712076", + "timestamp": "2026-06-17T09:04:58.756215188", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.5" @@ -34,7 +34,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.collapse.parquet:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -45,7 +45,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -56,7 +56,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.collapse.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -67,7 +67,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.pixelator-combine-collapse.log:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -87,7 +87,7 @@ [ "PIXELATOR_COMBINE_COLLAPSE", "pixelator", - "0.28.0" + "0.29.0" ] ], "log": [ @@ -95,7 +95,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.pixelator-combine-collapse.log:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -106,7 +106,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.collapse.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -117,7 +117,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.collapse.parquet:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -128,7 +128,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -138,15 +138,15 @@ [ "PIXELATOR_COMBINE_COLLAPSE", "pixelator", - "0.28.0" + "0.29.0" ] ] } ], - "timestamp": "2026-05-29T14:09:20.866006659", + "timestamp": "2026-06-17T09:04:43.24612248", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.2" + "nextflow": "25.10.5" } } } \ No newline at end of file diff --git a/modules/local/pixelator/demux/main.nf b/modules/local/pixelator/demux/main.nf index 2a3fc150..1fec85dd 100644 --- a/modules/local/pixelator/demux/main.nf +++ b/modules/local/pixelator/demux/main.nf @@ -6,8 +6,8 @@ process PIXELATOR_DEMUX { // conda "bioconda::pixelator=0.18.2" container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'quay.io/pixelgen-technologies/pixelator:0.28.0' - : 'quay.io/pixelgen-technologies/pixelator:0.28.0'}" + ? 'quay.io/pixelgen-technologies/pixelator:0.29.0' + : 'quay.io/pixelgen-technologies/pixelator:0.29.0'}" input: tuple val(meta), path(reads), path(panel_file), val(panel), val(design) diff --git a/modules/local/pixelator/demux/tests/main.nf.test b/modules/local/pixelator/demux/tests/main.nf.test index c4120c24..f773e525 100644 --- a/modules/local/pixelator/demux/tests/main.nf.test +++ b/modules/local/pixelator/demux/tests/main.nf.test @@ -18,10 +18,10 @@ nextflow_process { process { """ input[0] = [ - [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v2.0', technology:'proxiome-v2' ], - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/pool1.amplicon.fq.zst', checkIfExists: true), + [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-prerelease', technology:'proxiome-v2' ], + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/amplicon/pool1.amplicon.fq.zst', checkIfExists: true), [], - 'proxiome-v2-immuno-155-v2.0', + 'proxiome-v2-immuno-155-prerelease', 'proxiome-v2' ] """ @@ -44,10 +44,10 @@ nextflow_process { process { """ input[0] = [ - [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v2.0', technology:'proxiome-v2' ], - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/pool1.amplicon.fq.zst', checkIfExists: true), + [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-prerelease', technology:'proxiome-v2' ], + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/amplicon/pool1.amplicon.fq.zst', checkIfExists: true), [], - 'proxiome-v2-immuno-155-v2.0', + 'proxiome-v2-immuno-155-prerelease', 'proxiome-v2' ] """ @@ -79,10 +79,10 @@ nextflow_process { process { """ input[0] = [ - [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v2.0', technology:'proxiome-v2' ], - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/pool1.amplicon.fq.zst', checkIfExists: true), + [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-prerelease', technology:'proxiome-v2' ], + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/amplicon/pool1.amplicon.fq.zst', checkIfExists: true), [], - 'proxiome-v2-immuno-155-v2.0', + 'proxiome-v2-immuno-155-prerelease', 'proxiome-v2' ] """ diff --git a/modules/local/pixelator/demux/tests/main.nf.test.snap b/modules/local/pixelator/demux/tests/main.nf.test.snap index ed2d8618..b45944ca 100644 --- a/modules/local/pixelator/demux/tests/main.nf.test.snap +++ b/modules/local/pixelator/demux/tests/main.nf.test.snap @@ -20,11 +20,11 @@ [ "PIXELATOR_DEMUX", "pixelator", - "0.28.0" + "0.29.0" ] ] ], - "timestamp": "2026-05-27T13:32:21.146201688", + "timestamp": "2026-06-17T09:05:36.203013433", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.5" @@ -38,7 +38,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, [ @@ -52,7 +52,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.demux.passed.fq.zst:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -63,7 +63,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.demux.failed.fq.zst:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -74,7 +74,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -85,7 +85,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -96,7 +96,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.pixelator-demux.log:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -119,7 +119,7 @@ [ "PIXELATOR_DEMUX", "pixelator", - "0.28.0" + "0.29.0" ] ], "demuxed": [ @@ -127,7 +127,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, [ @@ -141,7 +141,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.demux.failed.fq.zst:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -152,7 +152,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.pixelator-demux.log:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -163,7 +163,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -174,7 +174,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.demux.passed.fq.zst:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -185,7 +185,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -195,15 +195,15 @@ [ "PIXELATOR_DEMUX", "pixelator", - "0.28.0" + "0.29.0" ] ] } ], - "timestamp": "2026-05-29T14:09:56.763402497", + "timestamp": "2026-06-17T09:05:07.592385053", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.2" + "nextflow": "25.10.5" } }, "PNA demux - multiple chunks": { @@ -241,11 +241,11 @@ [ "PIXELATOR_DEMUX", "pixelator", - "0.28.0" + "0.29.0" ] ] ], - "timestamp": "2026-05-27T13:32:50.971603605", + "timestamp": "2026-06-17T09:06:07.713814523", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.5" diff --git a/modules/local/pixelator/denoise/main.nf b/modules/local/pixelator/denoise/main.nf index 2648fdff..b325c3b5 100644 --- a/modules/local/pixelator/denoise/main.nf +++ b/modules/local/pixelator/denoise/main.nf @@ -6,8 +6,8 @@ process PIXELATOR_DENOISE { // conda "bioconda::pixelator=0.18.2" container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'quay.io/pixelgen-technologies/pixelator:0.28.0' - : 'quay.io/pixelgen-technologies/pixelator:0.28.0'}" + ? 'quay.io/pixelgen-technologies/pixelator:0.29.0' + : 'quay.io/pixelgen-technologies/pixelator:0.29.0'}" input: tuple val(meta), path(data) diff --git a/modules/local/pixelator/denoise/tests/main.nf.test b/modules/local/pixelator/denoise/tests/main.nf.test index d65220cf..a21df627 100644 --- a/modules/local/pixelator/denoise/tests/main.nf.test +++ b/modules/local/pixelator/denoise/tests/main.nf.test @@ -14,8 +14,8 @@ nextflow_process { process { """ input[0] = [ - [ id:'sample1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v2.0', technology:'proxiome-v2' ], - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/sample1.dehashed.pxl', checkIfExists: true), + [ id:'sample1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-prerelease', technology:'proxiome-v2' ], + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/sample_calling/sample1.dehashed.pxl', checkIfExists: true), ] """ } @@ -37,8 +37,8 @@ nextflow_process { process { """ input[0] = [ - [ id:'sample1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v2.0', technology:'proxiome-v2' ], - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/sample1.dehashed.pxl', checkIfExists: true), + [ id:'sample1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-prerelease', technology:'proxiome-v2' ], + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/sample_calling/sample1.dehashed.pxl', checkIfExists: true), ] """ } diff --git a/modules/local/pixelator/denoise/tests/main.nf.test.snap b/modules/local/pixelator/denoise/tests/main.nf.test.snap index 89961abd..2d525aec 100644 --- a/modules/local/pixelator/denoise/tests/main.nf.test.snap +++ b/modules/local/pixelator/denoise/tests/main.nf.test.snap @@ -16,11 +16,11 @@ [ "PIXELATOR_DENOISE", "pixelator", - "0.28.0" + "0.29.0" ] ] ], - "timestamp": "2026-05-27T13:33:14.143824133", + "timestamp": "2026-06-17T09:06:26.542202157", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.5" @@ -34,7 +34,7 @@ { "id": "sample1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "sample1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -45,7 +45,7 @@ { "id": "sample1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "sample1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -56,7 +56,7 @@ { "id": "sample1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "sample1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -67,7 +67,7 @@ { "id": "sample1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, [ @@ -82,7 +82,7 @@ { "id": "sample1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "sample1.pixelator-denoise.log:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -102,7 +102,7 @@ [ "PIXELATOR_DENOISE", "pixelator", - "0.28.0" + "0.29.0" ] ], "all_results": [ @@ -110,7 +110,7 @@ { "id": "sample1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, [ @@ -125,7 +125,7 @@ { "id": "sample1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "sample1.pixelator-denoise.log:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -136,7 +136,7 @@ { "id": "sample1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "sample1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -147,7 +147,7 @@ { "id": "sample1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "sample1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -158,7 +158,7 @@ { "id": "sample1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "sample1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -168,15 +168,15 @@ [ "PIXELATOR_DENOISE", "pixelator", - "0.28.0" + "0.29.0" ] ] } ], - "timestamp": "2026-05-29T14:11:33.356376368", + "timestamp": "2026-06-17T09:06:14.523138136", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.2" + "nextflow": "25.10.5" } } } \ No newline at end of file diff --git a/modules/local/pixelator/graph/main.nf b/modules/local/pixelator/graph/main.nf index b45bd253..5424bf1c 100644 --- a/modules/local/pixelator/graph/main.nf +++ b/modules/local/pixelator/graph/main.nf @@ -4,8 +4,8 @@ process PIXELATOR_GRAPH { label 'process_long' container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'quay.io/pixelgen-technologies/pixelator:0.28.0' - : 'quay.io/pixelgen-technologies/pixelator:0.28.0'}" + ? 'quay.io/pixelgen-technologies/pixelator:0.29.0' + : 'quay.io/pixelgen-technologies/pixelator:0.29.0'}" input: tuple val(meta), path(edge_list), path(panel_file), val(panel) diff --git a/modules/local/pixelator/graph/tests/main.nf.test b/modules/local/pixelator/graph/tests/main.nf.test index 65f519bd..99f1b03b 100644 --- a/modules/local/pixelator/graph/tests/main.nf.test +++ b/modules/local/pixelator/graph/tests/main.nf.test @@ -12,17 +12,13 @@ nextflow_process { options "-stub" when { - params { - pna_graph_component_size_min_threshold = 100 - } - process { """ input[0] = [ - [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v2.0', technology:'proxiome-v2' ], - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/pool1.collapse.parquet', checkIfExists: true), + [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-prerelease', technology:'proxiome-v2' ], + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/collapse/pool1.collapse.parquet', checkIfExists: true), [], - 'proxiome-v2-immuno-155-v2.0', + 'proxiome-v2-immuno-155-prerelease', ] """ } @@ -39,17 +35,19 @@ nextflow_process { test("PNA graph - small test") { when { params { - pna_graph_component_size_min_threshold = 100 + // Synthetic data was generated to pass with the test with lower than default resolution + pna_graph_refinement_stage_leiden_resolution = 0.01 + pna_graph_component_size_min_threshold = 100 outdir = "$outputDir" } process { """ input[0] = [ - [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v2.0', technology:'proxiome-v2' ], - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/pool1.collapse.parquet', checkIfExists: true), + [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-prerelease', technology:'proxiome-v2' ], + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/collapse/pool1.collapse.parquet', checkIfExists: true), [], - 'proxiome-v2-immuno-155-v2.0', + 'proxiome-v2-immuno-155-prerelease', ] """ } diff --git a/modules/local/pixelator/graph/tests/main.nf.test.snap b/modules/local/pixelator/graph/tests/main.nf.test.snap index ac7c1897..81e965c3 100644 --- a/modules/local/pixelator/graph/tests/main.nf.test.snap +++ b/modules/local/pixelator/graph/tests/main.nf.test.snap @@ -7,7 +7,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, [ @@ -22,7 +22,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -33,7 +33,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -44,7 +44,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -55,7 +55,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.pixelator-graph.log:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -75,7 +75,7 @@ [ "PIXELATOR_GRAPH", "pixelator", - "0.28.0" + "0.29.0" ] ], "all_results": [ @@ -83,7 +83,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, [ @@ -98,7 +98,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.pixelator-graph.log:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -109,7 +109,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -120,7 +120,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -131,7 +131,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -141,15 +141,15 @@ [ "PIXELATOR_GRAPH", "pixelator", - "0.28.0" + "0.29.0" ] ] } ], - "timestamp": "2026-05-29T14:12:15.612838605", + "timestamp": "2026-06-17T09:06:33.227014884", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.2" + "nextflow": "25.10.5" } }, "PNA graph - small test": { @@ -170,11 +170,11 @@ [ "PIXELATOR_GRAPH", "pixelator", - "0.28.0" + "0.29.0" ] ] ], - "timestamp": "2026-05-27T13:33:43.258292043", + "timestamp": "2026-06-17T09:06:47.873445645", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.5" diff --git a/modules/local/pixelator/layout/main.nf b/modules/local/pixelator/layout/main.nf index 6a929361..112d4e0e 100644 --- a/modules/local/pixelator/layout/main.nf +++ b/modules/local/pixelator/layout/main.nf @@ -5,8 +5,8 @@ process PIXELATOR_LAYOUT { // TODO: Add conda // conda "bioconda::pixelator=0.18.2" container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'quay.io/pixelgen-technologies/pixelator:0.28.0' - : 'quay.io/pixelgen-technologies/pixelator:0.28.0'}" + ? 'quay.io/pixelgen-technologies/pixelator:0.29.0' + : 'quay.io/pixelgen-technologies/pixelator:0.29.0'}" input: tuple val(meta), path(data) diff --git a/modules/local/pixelator/layout/tests/main.nf.test b/modules/local/pixelator/layout/tests/main.nf.test index 061ca58f..3a37ae7a 100644 --- a/modules/local/pixelator/layout/tests/main.nf.test +++ b/modules/local/pixelator/layout/tests/main.nf.test @@ -15,14 +15,14 @@ nextflow_process { when { params { save_all = true - layout_algorithm = "pmds_3d" + pna_layout_layout_algorithm = "coarsened_pmds_3d" skip_layout = false } process { """ input[0] = [ - [ id:'sample1', design: 'proxiome-v2', panel:'proxiome-v2-immuno-155-v2.0', technology:'proxiome-v2' ], - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/sample1.analysis.pxl', checkIfExists: true) + [ id:'sample1', design: 'proxiome-v2', panel:'proxiome-v2-immuno-155-prerelease', technology:'proxiome-v2' ], + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/analysis/sample1.analysis.pxl', checkIfExists: true) ] """ } @@ -40,15 +40,15 @@ nextflow_process { when { params { save_all = true - layout_algorithm = "pmds_3d" + pna_layout_layout_algorithm = "coarsened_pmds_3d" skip_layout = false outdir = "$outputDir" } process { """ input[0] = [ - [ id:'sample1', design: 'proxiome-v2', panel:'proxiome-v2-immuno-155-v2.0', technology:'proxiome-v2' ], - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/sample1.analysis.pxl', checkIfExists: true) + [ id:'sample1', design: 'proxiome-v2', panel:'proxiome-v2-immuno-155-prerelease', technology:'proxiome-v2' ], + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/analysis/sample1.analysis.pxl', checkIfExists: true) ] """ } diff --git a/modules/local/pixelator/layout/tests/main.nf.test.snap b/modules/local/pixelator/layout/tests/main.nf.test.snap index b291871e..8afecb97 100644 --- a/modules/local/pixelator/layout/tests/main.nf.test.snap +++ b/modules/local/pixelator/layout/tests/main.nf.test.snap @@ -17,11 +17,11 @@ [ "PIXELATOR_LAYOUT", "pixelator", - "0.28.0" + "0.29.0" ] ] ], - "timestamp": "2026-05-27T13:34:08.047886362", + "timestamp": "2026-06-17T08:46:03.122789993", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.5" @@ -35,7 +35,7 @@ { "id": "sample1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "sample1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -46,7 +46,7 @@ { "id": "sample1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "sample1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -57,7 +57,7 @@ { "id": "sample1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "sample1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -68,7 +68,7 @@ { "id": "sample1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, [ @@ -83,7 +83,7 @@ { "id": "sample1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "sample1.pixelator-layout.log:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -103,7 +103,7 @@ [ "PIXELATOR_LAYOUT", "pixelator", - "0.28.0" + "0.29.0" ] ], "all_results": [ @@ -111,7 +111,7 @@ { "id": "sample1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, [ @@ -126,7 +126,7 @@ { "id": "sample1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "sample1.pixelator-layout.log:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -137,7 +137,7 @@ { "id": "sample1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "sample1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -148,7 +148,7 @@ { "id": "sample1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "sample1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -159,7 +159,7 @@ { "id": "sample1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "sample1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -169,15 +169,15 @@ [ "PIXELATOR_LAYOUT", "pixelator", - "0.28.0" + "0.29.0" ] ] } ], - "timestamp": "2026-05-29T14:13:11.19895797", + "timestamp": "2026-06-17T08:45:50.89566387", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.2" + "nextflow": "25.10.5" } } } \ No newline at end of file diff --git a/modules/local/pixelator/list_options/main.nf b/modules/local/pixelator/list_options/main.nf index ae5e0241..13e4796f 100644 --- a/modules/local/pixelator/list_options/main.nf +++ b/modules/local/pixelator/list_options/main.nf @@ -5,8 +5,8 @@ process PIXELATOR_LIST_OPTIONS { // TODO: Add conda back // conda "${moduleDir}/environment.yml" container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'quay.io/pixelgen-technologies/pixelator:0.28.0' - : 'quay.io/pixelgen-technologies/pixelator:0.28.0'}" + ? 'quay.io/pixelgen-technologies/pixelator:0.29.0' + : 'quay.io/pixelgen-technologies/pixelator:0.29.0'}" output: path "design_options.txt", emit: designs @@ -34,6 +34,7 @@ process PIXELATOR_LIST_OPTIONS { cat <<-END_PANELS > panel_options.txt proxiome-v1-immuno-155-v1.1 + proxiome-v2-immuno-155-prerelease proxiome-v2-immuno-155-v2.0 END_PANELS """ diff --git a/modules/local/pixelator/sample_calling/main.nf b/modules/local/pixelator/sample_calling/main.nf index 75c69ac4..dbb2ccd0 100644 --- a/modules/local/pixelator/sample_calling/main.nf +++ b/modules/local/pixelator/sample_calling/main.nf @@ -5,8 +5,8 @@ process PIXELATOR_SAMPLE_CALLING { // TODO: Add conda // conda "bioconda::pixelator=0.18.2" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'quay.io/pixelgen-technologies/pixelator:0.28.0' - : 'quay.io/pixelgen-technologies/pixelator:0.28.0'}" + ? 'quay.io/pixelgen-technologies/pixelator:0.29.0' + : 'quay.io/pixelgen-technologies/pixelator:0.29.0'}" input: tuple val(meta), path(data), path(samplesheet) diff --git a/modules/local/pixelator/sample_calling/tests/main.nf.test b/modules/local/pixelator/sample_calling/tests/main.nf.test index b3964d4f..7af1292d 100644 --- a/modules/local/pixelator/sample_calling/tests/main.nf.test +++ b/modules/local/pixelator/sample_calling/tests/main.nf.test @@ -15,9 +15,9 @@ nextflow_process { process { """ input[0] = [ - [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v2.0', technology:'proxiome-v2' ], - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/pool1.graph.pxl', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'samplesheet/pna/samplesheet_proxiome_v2.csv', checkIfExists: true), + [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-prerelease', technology:'proxiome-v2' ], + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/graph/pool1.graph.pxl', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/samplesheet/pna/samplesheet_proxiome_v2.csv', checkIfExists: true), ] """ } @@ -39,9 +39,9 @@ nextflow_process { process { """ input[0] = [ - [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v2.0', technology:'proxiome-v2' ], - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/pool1.graph.pxl', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'samplesheet/pna/samplesheet_proxiome_v2.csv', checkIfExists: true), + [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-prerelease', technology:'proxiome-v2' ], + file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/graph/pool1.graph.pxl', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/samplesheet/pna/samplesheet_proxiome_v2.csv', checkIfExists: true), ] """ } diff --git a/modules/local/pixelator/sample_calling/tests/main.nf.test.snap b/modules/local/pixelator/sample_calling/tests/main.nf.test.snap index d5bca131..01989ae3 100644 --- a/modules/local/pixelator/sample_calling/tests/main.nf.test.snap +++ b/modules/local/pixelator/sample_calling/tests/main.nf.test.snap @@ -35,7 +35,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, [ @@ -51,7 +51,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.sample_calling.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -62,7 +62,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.sample_calling.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -73,7 +73,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, [ @@ -91,7 +91,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.pixelator-sample-calling.log:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -111,14 +111,14 @@ ] ], "6": [ - "versions.yml:md5,caecdbbf67cdc742583ac0658769573d" + "versions.yml:md5,eded59c796dbb279d76d4afebfaf20be" ], "all_results": [ [ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, [ @@ -136,7 +136,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.pixelator-sample-calling.log:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -147,7 +147,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.sample_calling.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -158,7 +158,7 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, [ @@ -174,21 +174,21 @@ { "id": "pool1", "design": "proxiome-v2", - "panel": "proxiome-v2-immuno-155-v2.0", + "panel": "proxiome-v2-immuno-155-prerelease", "technology": "proxiome-v2" }, "pool1.sample_calling.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions": [ - "versions.yml:md5,caecdbbf67cdc742583ac0658769573d" + "versions.yml:md5,eded59c796dbb279d76d4afebfaf20be" ] } ], - "timestamp": "2026-05-29T14:13:36.808454251", + "timestamp": "2026-06-17T09:07:17.066066904", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.2" + "nextflow": "25.10.5" } } } \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 937996fb..33c221d5 100644 --- a/nextflow.config +++ b/nextflow.config @@ -61,20 +61,21 @@ params { // PNA graph pna_graph_multiplet_recovery = true pna_graph_initial_stage_leiden_resolution = 1.0 - pna_graph_refinement_stage_leiden_resolution = 0.01 + pna_graph_refinement_stage_leiden_resolution = 0.5 pna_graph_min_count = 1 pna_graph_max_refinement_recursion_depth = 3 pna_graph_edge_cycle_verification = true pna_graph_initial_stage_max_edges_to_remove = 10 - pna_graph_refinement_stage_max_edges_to_remove = 10 + pna_graph_refinement_stage_max_edges_to_remove = 20 pna_graph_initial_stage_max_edges_to_remove_relative = null pna_graph_refinement_stage_max_edges_to_remove_relative = null pna_graph_component_size_min_threshold = 8000 + pna_graph_component_size_max_threshold = 500000 // sample-calling options pna_sample_calling_remove_incompatible = true pna_sample_calling_save_undetermined = false - pna_sample_calling_confidence_threshold = 0.9 + pna_sample_calling_enrichment_threshold = 10.0 // PNA denoise pna_denoise_run_one_core_graph_denoising = false @@ -96,7 +97,7 @@ params { // PNA layout pna_layout_no_node_marker_counts = false - pna_layout_layout_algorithm = "wpmds_3d" + pna_layout_layout_algorithm = "coarsened_pmds_3d" pna_layout_pmds_pivots = 50 pna_layout_wpmds_k = 5 skip_layout = false @@ -119,7 +120,8 @@ params { help_full = false show_hidden = false version = false - pipelines_testdata_base_path = System.getenv('NFT_TESTDATA_BASE_PATH') ?: 'https://raw.githubusercontent.com/nf-core/test-datasets/pixelator/' + // pipelines_testdata_base_path points to a specific commit on the pixelator branch of the nf-core/test-datasets repo + pipelines_testdata_base_path = System.getenv('NFT_TESTDATA_BASE_PATH') ?: 'https://raw.githubusercontent.com/nf-core/test-datasets/e8950f260973a6778e2ff24988e12fd4474d60e1/' modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' trace_report_suffix = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss') @@ -288,6 +290,8 @@ profiles { // Load nf-core custom profiles from different institutions includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" +includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/pixelator.config" : "/dev/null" + // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled // Set to your registry if you have a mirror of containers @@ -375,7 +379,7 @@ manifest { mainScript = 'main.nf' defaultBranch = 'master' nextflowVersion = '!>=25.10.4' - version = '4.1.2' + version = '5.0.0' doi = '10.1101/2023.06.05.543770' } diff --git a/nextflow_schema.json b/nextflow_schema.json index 7ae7f5bc..ddd0a6da 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -225,7 +225,7 @@ "help": "This should typically be set higher than the refinement stage resolution." }, "pna_graph_refinement_stage_leiden_resolution": { - "default": 0.01, + "default": 0.5, "fa_icon": "fas fa-sliders-h", "minimum": 0, "type": "number", @@ -265,7 +265,7 @@ "pna_graph_refinement_stage_max_edges_to_remove": { "type": "integer", "fa_icon": "fas fa-trash", - "default": 10, + "default": 20, "minimum": 1, "description": "The maximum number of edges to remove between components during the refinement stage (iteration > 0) of multiplet recovery." }, @@ -287,6 +287,13 @@ "minimum": 1, "default": 8000, "description": "Components with fewer nodes than this will be filtered from the output data. Set to null to enable automatic size filtering based on the data." + }, + "pna_graph_component_size_max_threshold": { + "type": "integer", + "fa_icon": "fas fa-compress-alt", + "minimum": 1, + "default": 500000, + "description": "Components with more nodes than this will be filtered from the output data. Set to null to enable automatic size filtering based on the data." } } }, @@ -312,14 +319,13 @@ "description": "Remove antibodies that are incompatible with their component's called sample.", "default": true }, - "pna_sample_calling_confidence_threshold": { + "pna_sample_calling_enrichment_threshold": { "type": "number", "fa_icon": "fas fa-percentage", - "description": "Confidence threshold for sample calling.", - "help_text": "Components with a sample confidence below this threshold will be considered undetermined.", - "default": 0.9, - "minimum": 0.0, - "maximum": 1.0 + "description": "Enrichment threshold for sample calling.", + "help_text": "Components with a sample enrichment below this threshold will be considered undetermined.", + "default": 10.0, + "minimum": 1.0 } } }, @@ -453,11 +459,11 @@ "type": "boolean" }, "pna_layout_layout_algorithm": { - "description": "Select a layout algorithm to use. This can be specified as a comma separated list to compute multiple layouts. Possible values are: pmds, pmds_3d, wpmds, wpmds_3d.", + "description": "Select a layout algorithm to use. This can be specified as a comma separated list to compute multiple layouts. Possible values are: pmds, pmds_3d, wpmds, wpmds_3d, coarsened_pmds_3d.", "fa_icon": "fas fa-project-diagram", "type": "string", - "enum": ["pmds_3d", "wpmds_3d"], - "default": "wpmds_3d" + "enum": ["pmds_3d", "wpmds_3d", "coarsened_pmds_3d"], + "default": "coarsened_pmds_3d" }, "pna_layout_pmds_pivots": { "type": "integer", @@ -627,8 +633,8 @@ "pipelines_testdata_base_path": { "type": "string", "fa_icon": "far fa-check-circle", - "description": "Base URL or local path to location of pipeline test dataset files", - "default": "https://raw.githubusercontent.com/nf-core/test-datasets/pixelator/", + "description": "Base URL or local path to location of pipeline test dataset files.", + "default": "https://raw.githubusercontent.com/nf-core/test-datasets/e8950f260973a6778e2ff24988e12fd4474d60e1/", "hidden": true }, "modules_testdata_base_path": { diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 05319757..e6a33cec 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,7 +22,7 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "Stable", - "datePublished": "2026-06-04T07:56:31+00:00", + "datePublished": "2026-07-13T06:29:10+00:00", "description": "

\n \n \n \"nf-core/pixelator\"\n \n

\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/pixelator)\n[![GitHub Actions CI Status](https://github.com/nf-core/pixelator/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/pixelator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/linting.yml)\n[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/pixelator/results)\n[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.10015112-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.10015112)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/pixelator)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23pixelator-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/pixelator)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/pixelator** is a bioinformatics best-practice analysis pipeline for analysis of data from the\nProximity Network (PNA) assay. It takes a samplesheet as input and will process your data\nusing `pixelator` to produce a PXL file containing single-cell protein abundance and protein interactomics data.\n\n![](./docs/images/nf-core-pixelator-metromap.svg)\n\nThe pipeline will run the following steps:\n\n1. Do quality control checks of input reads and build amplicons ([`pixelator single-cell-pna amplicon`](https://github.com/PixelgenTechnologies/pixelator))\n2. Create groups of amplicons based on their marker assignments ([`pixelator single-cell-pna demux`](https://github.com/PixelgenTechnologies/pixelator))\n3. Derive original molecules to use as edge list downstream by error correcting, and counting input amplicons ([`pixelator single-cell-pna collapse`](https://github.com/PixelgenTechnologies/pixelator))\n4. Compute the components of the graph from the edge list in order to create putative cells ([`pixelator single-cell-pna graph`](https://github.com/PixelgenTechnologies/pixelator))\n5. _(Conditional; only for PNA hashed data)_ Assign components to samples in pooled experiments ([`pixelator single-cell-pna sample-calling`](https://github.com/PixelgenTechnologies/pixelator))\n6. Denoise the cell graphs ([`pixelator single-cell-pna denoise`](https://github.com/PixelgenTechnologies/pixelator))\n7. Analyze the spatial information in the cell graphs ([`pixelator single-cell-pna analysis`](https://github.com/PixelgenTechnologies/pixelator))\n8. Generate 3D graph layouts for visualization of cells ([`pixelator single-cell-pna layout`](https://github.com/PixelgenTechnologies/pixelator))\n9. Proxiome Experiment Summary generation using [PixelatorES](https://github.com/PixelgenTechnologies/pixelatorES)\n\n> [!NOTE]\n> If you are looking to run the pipeline with Molecular Pixelation (MPX) data. Please refer to the [release 2.3.1](https://nf-co.re/pixelator/2.3.1/),\n> which is the last version to support that data type.\n\n> [!WARNING]\n> Since Nextflow 23.07.0-edge, Nextflow no longer mounts the host's home directory when using Apptainer or Singularity.\n> This causes issues in some dependencies. As a workaround, you can revert to the old behavior by setting the environment variable\n> `NXF_APPTAINER_HOME_MOUNT` or `NXF_SINGULARITY_HOME_MOUNT` to `true` in the machine from which you launch the pipeline.\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows (the exact values you need to input depend on the design and panel you are using - please see [https://nf-co.re/pixelator/usage](https://nf-co.re/pixelator/usage) for more details).\nFor hashed PNA data (Proxiome kit v2), the samplesheet will look as follows:\n\n`samplesheet.csv`:\n\n```csv\npool,hash_index,sample,sample_alias,condition,design,panel,fastq_1,fastq_2\npool1,1,sample1,s1,control,proxiome-v2,proxiome-v2-immuno-155-v2.0,pool1_R1_001.fastq.gz,pool1_R2_001.fastq.gz\npool1,2,sample2,s2,case,proxiome-v2,proxiome-v2-immuno-155-v2.0,pool1_R1_001.fastq.gz,pool1_R2_001.fastq.gz\npool2,1,sample3,s3,control,proxiome-v2,proxiome-v2-immuno-155-v2.0,pool2_R1_001.fastq.gz,pool2_R2_001.fastq.gz\n```\n\n> [!NOTE]\n> For an example with non-hashed PNA data (Proxiome kit v1), see [Proxiome v1 samplesheet](../assets/example_samplesheet_proxiome_v1.csv)\n\n> [!WARNING]\n> Panel and design names have been completely renamed in pixelator 0.26\n> (nf-core/pixelator 4.0 and above). Refer to the pixelator\n> [changelog](https://github.com/PixelgenTechnologies/pixelator/releases/tag/v0.26.0)\n> for more details.\n\nEach row represents a sample and gives the design, a panel file and the input fastq files.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/pixelator \\\n -profile , \\\n --technology \n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> This version of the pipeline does not support conda environments, due to issues with upstream dependencies.\n> This means you cannot use the `conda` and `mamba` profiles. Please use `docker` or `singularity` instead.\n> We hope to add support for conda environments in the future.\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/pixelator/usage) and the [parameter documentation](https://nf-co.re/pixelator/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/pixelator/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/pixelator/output).\n\n## Credits\n\nnf-core/pixelator was originally written for [Pixelgen Technologies AB](https://www.pixelgen.com/) by:\n\n- Florian De Temmerman\n- Johan Dahlberg\n- Alvaro Martinez Barrio\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#pixelator` channel](https://nfcore.slack.com/channels/pixelator) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/pixelator for your analysis, please cite it using the following doi: [10.5281/zenodo.10015112](https://doi.org/10.5281/zenodo.10015112)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n\nYou can cite the Proximity Network Technology as follows:\n\n> **Single-Cell Protein Interactomes by the Proximity Network Assay.**\n>\n> Filip Karlsson, Michele Simonetti, Christina Galonska, Max Karlsson, Hanna van Ooijen, Tomasz Kallas, Divya Thiagarajan, Maud Schweitzer, Ludvig Larsson, Vincent van Hoef, Pouria Tajvar, Johan Dahlberg, Florian De Temmerman, Louise Leijonancker, Sylvain Geny, Rikard Forlin, Erika Negrini, Stefan Petkov, Lovisa Franz\u00e9n, Jessica Bunz, Christine Moge, Henrik Everberg, Petter Brodin, Alvaro Martinez Barrio, Simon Fredriksson\n>\n> _bioRxiv_ 2025.06.19.660329; doi: [10.1101/2025.06.19.660329](https://doi.org/10.1101/2025.06.19.660329)\n", "hasPart": [ { @@ -102,7 +102,7 @@ }, "mentions": [ { - "@id": "#047d5a72-e822-45cc-8115-f31953cae2be" + "@id": "#4d70a5db-5ef1-410a-821e-b4562c507ed1" } ], "name": "nf-core/pixelator" @@ -129,19 +129,21 @@ "SoftwareSourceCode", "ComputationalWorkflow" ], - "creator": [ + "author": [ { "@id": "https://orcid.org/0009-0006-0086-2470" - }, + } + ], + "contributor": [ { - "@id": "#johan.dahlberg@pixelgen.tech" + "@id": "https://orcid.org/0000-0001-6962-1460" }, { - "@id": "https://orcid.org/0000-0003-2702-1103" + "@id": "https://orcid.org/0000-0001-5064-2093" } ], "dateCreated": "", - "dateModified": "2026-06-04T07:56:31Z", + "dateModified": "2026-07-13T08:29:10Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -159,9 +161,6 @@ "maintainer": [ { "@id": "https://orcid.org/0009-0006-0086-2470" - }, - { - "@id": "#johan.dahlberg@pixelgen.tech" } ], "name": [ @@ -175,10 +174,10 @@ }, "url": [ "https://github.com/nf-core/pixelator", - "https://nf-co.re/pixelator/4.1.2/" + "https://nf-co.re/pixelator/5.0.0/" ], "version": [ - "4.1.2" + "5.0.0" ] }, { @@ -194,11 +193,11 @@ "version": "!>=25.10.4" }, { - "@id": "#047d5a72-e822-45cc-8115-f31953cae2be", + "@id": "#4d70a5db-5ef1-410a-821e-b4562c507ed1", "@type": "TestSuite", "instance": [ { - "@id": "#b5a6d21f-6754-4699-931f-3a07a23b0818" + "@id": "#2f33b14a-39f3-4277-8f0c-5c2036a43877" } ], "mainEntity": { @@ -207,7 +206,7 @@ "name": "Test suite for nf-core/pixelator" }, { - "@id": "#b5a6d21f-6754-4699-931f-3a07a23b0818", + "@id": "#2f33b14a-39f3-4277-8f0c-5c2036a43877", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/pixelator", "resource": "repos/nf-core/pixelator/actions/workflows/nf-test.yml", @@ -343,20 +342,26 @@ { "@id": "https://orcid.org/0009-0006-0086-2470", "@type": "Person", + "affiliation": "Pixelgen Technologies AB", "email": "florian.detemmerman@pixelgen.com", - "name": "Florian De Temmerman" + "name": "Florian De Temmerman", + "url": "https://github.com/fbdtemme" }, { - "@id": "#johan.dahlberg@pixelgen.tech", + "@id": "https://orcid.org/0000-0001-6962-1460", "@type": "Person", - "email": "johan.dahlberg@pixelgen.tech", - "name": "Johan Dahlberg" + "affiliation": "Pixelgen Technologies AB", + "email": "johan.dahlberg@pixelgen.com", + "name": "Johan Dahlberg", + "url": "https://github.com/johandahlberg" }, { - "@id": "https://orcid.org/0000-0003-2702-1103", + "@id": "https://orcid.org/0000-0001-5064-2093", "@type": "Person", - "email": "adrien.coulier@pixelgen.com", - "name": "Adrien Coulier" + "affiliation": "Pixelgen Technologies AB", + "email": "alvaro.martinez.barrio@pixelgen.com", + "name": "Alvaro Martinez Barrio", + "url": "https://github.com/ambarrio" } ] } \ No newline at end of file diff --git a/subworkflows/local/pna/v1/tests/main.nf.test b/subworkflows/local/pna/v1/tests/main.nf.test index 660477a1..89bb6fdb 100644 --- a/subworkflows/local/pna/v1/tests/main.nf.test +++ b/subworkflows/local/pna/v1/tests/main.nf.test @@ -25,8 +25,8 @@ nextflow_workflow { input[0] = Channel.of([ meta, [ - file(params.pipelines_testdata_base_path + 'testdata/pna/fastq/sample1_R1.fastq.gz', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/fastq/sample1_R2.fastq.gz', checkIfExists: true) + file(params.pipelines_testdata_base_path + 'new-test-data/pna/fastq/sample1_R1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/fastq/sample1_R2.fastq.gz', checkIfExists: true) ] ]) input[1] = Channel.of([meta, []]) diff --git a/subworkflows/local/pna/v1/tests/main.nf.test.snap b/subworkflows/local/pna/v1/tests/main.nf.test.snap index 8078d9d0..39be890f 100644 --- a/subworkflows/local/pna/v1/tests/main.nf.test.snap +++ b/subworkflows/local/pna/v1/tests/main.nf.test.snap @@ -93,10 +93,10 @@ "pixelator/logs/sample1.pixelator-layout.log" ] ], - "timestamp": "2026-05-21T13:27:10.984127921", + "timestamp": "2026-06-17T09:32:41.349343247", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.0" + "nextflow": "25.10.5" } } } \ No newline at end of file diff --git a/subworkflows/local/pna/v2/tests/main.nf.test b/subworkflows/local/pna/v2/tests/main.nf.test index 14f4ee69..d9f76937 100644 --- a/subworkflows/local/pna/v2/tests/main.nf.test +++ b/subworkflows/local/pna/v2/tests/main.nf.test @@ -10,7 +10,7 @@ nextflow_workflow { tag "pixelator" tag "pixelator/pna" - test("Default parameters [design: proxiome-v2, panel: proxiome-v2-immuno-155-v2.0]") { + test("Default parameters [design: proxiome-v2, panel: proxiome-v2-immuno-155-prerelease]") { when { params { @@ -21,12 +21,12 @@ nextflow_workflow { workflow { """ - def meta = [ pool:'pool1', id:'sample1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v2.0', technology:'proxiome-v1' ] + def meta = [ pool:'pool1', id:'sample1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-prerelease', technology:'proxiome-v2' ] input[0] = Channel.of([ meta, [ - file(params.pipelines_testdata_base_path + 'testdata/pna/fastq/pool1_R1.fastq.gz', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/fastq/pool1_R2.fastq.gz', checkIfExists: true) + file(params.pipelines_testdata_base_path + 'new-test-data/pna/fastq/pool1_R1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'new-test-data/pna/fastq/pool1_R2.fastq.gz', checkIfExists: true) ] ]) input[1] = Channel.of([meta, []]) diff --git a/subworkflows/local/pna/v2/tests/main.nf.test.snap b/subworkflows/local/pna/v2/tests/main.nf.test.snap index 62187a58..5fff2ec5 100644 --- a/subworkflows/local/pna/v2/tests/main.nf.test.snap +++ b/subworkflows/local/pna/v2/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "Default parameters [design: proxiome-v2, panel: proxiome-v2-immuno-155-v2.0]": { + "Default parameters [design: proxiome-v2, panel: proxiome-v2-immuno-155-prerelease]": { "content": [ 22, [ @@ -112,10 +112,10 @@ "pixelator/sample_calling/sample2.report.json" ] ], - "timestamp": "2026-05-29T14:13:13.181930826", + "timestamp": "2026-06-17T09:32:39.539686784", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.2" + "nextflow": "25.10.5" } } } \ No newline at end of file diff --git a/tests/nextflow.config b/tests/nextflow.config index 1e12f8a5..3d008999 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -5,7 +5,8 @@ */ params { - pipelines_testdata_base_path = System.getenv('NFT_TESTDATA_BASE_PATH') ?: "https://raw.githubusercontent.com/nf-core/test-datasets/pixelator/" + // Default should point to a specific commit on github.com/nf-core/test-datasets, branch pixelator + pipelines_testdata_base_path = System.getenv('NFT_TESTDATA_BASE_PATH') ?: "https://raw.githubusercontent.com/nf-core/test-datasets/e8950f260973a6778e2ff24988e12fd4474d60e1/" modules_testdata_base_path = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/" outdir = 'results' } diff --git a/tests/proxiome_v1.nf.test.snap b/tests/proxiome_v1.nf.test.snap index 90b8ccf0..5d208642 100644 --- a/tests/proxiome_v1.nf.test.snap +++ b/tests/proxiome_v1.nf.test.snap @@ -114,41 +114,41 @@ "cat": 9.5 }, "EXPERIMENT_SUMMARY": { - "experiment-summary": "0.10.4" + "experiment-summary": "0.11.2" }, "PIXELATOR_AMPLICON": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "PIXELATOR_ANALYSIS": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "PIXELATOR_COLLAPSE": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "PIXELATOR_COMBINE_COLLAPSE": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "PIXELATOR_DEMUX": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "PIXELATOR_DENOISE": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "PIXELATOR_GRAPH": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "PIXELATOR_LAYOUT": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "PIXELATOR_LIST_OPTIONS": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "Workflow": { - "nf-core/pixelator": "v4.1.2" + "nf-core/pixelator": "v5.0.0" } } ], - "timestamp": "2026-06-04T08:06:20.429989163", + "timestamp": "2026-06-17T09:05:52.731272619", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.5" @@ -162,37 +162,37 @@ "cat": 9.5 }, "EXPERIMENT_SUMMARY": { - "experiment-summary": "0.10.4" + "experiment-summary": "0.11.2" }, "PIXELATOR_AMPLICON": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "PIXELATOR_ANALYSIS": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "PIXELATOR_COLLAPSE": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "PIXELATOR_COMBINE_COLLAPSE": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "PIXELATOR_DEMUX": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "PIXELATOR_DENOISE": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "PIXELATOR_GRAPH": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "PIXELATOR_LAYOUT": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "PIXELATOR_LIST_OPTIONS": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "Workflow": { - "nf-core/pixelator": "v4.1.2" + "nf-core/pixelator": "v5.0.0" } }, [ @@ -295,16 +295,16 @@ "sample_2.meta.json:md5,e0b756a91edb80e878baa6862b2c3c6d", "sample_1.meta.json:md5,eb91c047c438beb4c746cf2acba39ab5", "sample_2.meta.json:md5,eb91c047c438beb4c746cf2acba39ab5", - "sample_1.meta.json:md5,9499ef2af613d6fa5cba5c91a443c726", - "sample_2.meta.json:md5,d73dc0fcfaaac01957e4611c89ef3dec", + "sample_1.meta.json:md5,1bab90d8bd4e8c054d11f1c51c94c9b1", + "sample_2.meta.json:md5,4d11b62a832866d52a2a0461ceebfcb5", "sample_1.meta.json:md5,82fcbb6ae5e3156c70978973c862f5f3", "sample_2.meta.json:md5,82fcbb6ae5e3156c70978973c862f5f3" ] ], - "timestamp": "2026-06-04T08:05:33.528022276", + "timestamp": "2026-07-15T11:34:04.157604261", "meta": { "nf-test": "0.9.5", - "nextflow": "25.10.5" + "nextflow": "26.04.2" } } } \ No newline at end of file diff --git a/tests/proxiome_v2.nf.test.snap b/tests/proxiome_v2.nf.test.snap index 225387e2..c2cd4ce4 100644 --- a/tests/proxiome_v2.nf.test.snap +++ b/tests/proxiome_v2.nf.test.snap @@ -151,41 +151,41 @@ "cat": 9.5 }, "EXPERIMENT_SUMMARY": { - "experiment-summary": "0.10.4" + "experiment-summary": "0.11.2" }, "PIXELATOR_AMPLICON": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "PIXELATOR_ANALYSIS": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "PIXELATOR_COLLAPSE": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "PIXELATOR_COMBINE_COLLAPSE": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "PIXELATOR_DEMUX": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "PIXELATOR_DENOISE": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "PIXELATOR_GRAPH": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "PIXELATOR_LAYOUT": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "PIXELATOR_LIST_OPTIONS": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "Workflow": { - "nf-core/pixelator": "v4.1.2" + "nf-core/pixelator": "v5.0.0" } } ], - "timestamp": "2026-06-04T08:06:34.673086328", + "timestamp": "2026-06-17T09:05:47.167686428", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.5" @@ -199,37 +199,37 @@ "cat": 9.5 }, "EXPERIMENT_SUMMARY": { - "experiment-summary": "0.10.4" + "experiment-summary": "0.11.2" }, "PIXELATOR_AMPLICON": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "PIXELATOR_ANALYSIS": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "PIXELATOR_COLLAPSE": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "PIXELATOR_COMBINE_COLLAPSE": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "PIXELATOR_DEMUX": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "PIXELATOR_DENOISE": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "PIXELATOR_GRAPH": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "PIXELATOR_LAYOUT": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "PIXELATOR_LIST_OPTIONS": { - "pixelator": "0.28.0" + "pixelator": "0.29.0" }, "Workflow": { - "nf-core/pixelator": "v4.1.2" + "nf-core/pixelator": "v5.0.0" } }, [ @@ -371,28 +371,28 @@ "sample2.meta.json:md5,2a6eaa66228775591525f74416f0b87f", "sample3.meta.json:md5,2a6eaa66228775591525f74416f0b87f", "sample4.meta.json:md5,2a6eaa66228775591525f74416f0b87f", - "pool1.meta.json:md5,bd2cd0b99effc41abbed806d3978d0cb", - "pool2.meta.json:md5,bd2cd0b99effc41abbed806d3978d0cb", + "pool1.meta.json:md5,236a76417f95f0c289a226753df41340", + "pool2.meta.json:md5,236a76417f95f0c289a226753df41340", "pool1.meta.json:md5,eb91c047c438beb4c746cf2acba39ab5", "pool2.meta.json:md5,eb91c047c438beb4c746cf2acba39ab5", - "pool1.meta.json:md5,0047bd705d96abde146ae6692a6a8d9b", - "pool2.meta.json:md5,0047bd705d96abde146ae6692a6a8d9b", + "pool1.meta.json:md5,d5e990e3a27ab9934bceeca516f1dbe5", + "pool2.meta.json:md5,d5e990e3a27ab9934bceeca516f1dbe5", "sample1.meta.json:md5,82fcbb6ae5e3156c70978973c862f5f3", "sample2.meta.json:md5,82fcbb6ae5e3156c70978973c862f5f3", "sample3.meta.json:md5,82fcbb6ae5e3156c70978973c862f5f3", "sample4.meta.json:md5,82fcbb6ae5e3156c70978973c862f5f3", - "pool1_undetermined.meta.json:md5,f59cd8963a4760d34bd2b41e740242b7", - "pool2_undetermined.meta.json:md5,f59cd8963a4760d34bd2b41e740242b7", - "sample1.meta.json:md5,f59cd8963a4760d34bd2b41e740242b7", - "sample2.meta.json:md5,f59cd8963a4760d34bd2b41e740242b7", - "sample3.meta.json:md5,f59cd8963a4760d34bd2b41e740242b7", - "sample4.meta.json:md5,f59cd8963a4760d34bd2b41e740242b7" + "pool1_undetermined.meta.json:md5,1c94e4736d2cf4a7f1960e85872f21fa", + "pool2_undetermined.meta.json:md5,1c94e4736d2cf4a7f1960e85872f21fa", + "sample1.meta.json:md5,1c94e4736d2cf4a7f1960e85872f21fa", + "sample2.meta.json:md5,1c94e4736d2cf4a7f1960e85872f21fa", + "sample3.meta.json:md5,1c94e4736d2cf4a7f1960e85872f21fa", + "sample4.meta.json:md5,1c94e4736d2cf4a7f1960e85872f21fa" ] ], - 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